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- EMDB-30832: CALHM1 close state with ordered CTH -

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Basic information

Entry
Database: EMDB / ID: EMD-30832
TitleCALHM1 close state with ordered CTH
Map dataEM map
Sample
  • Organelle or cellular component: CALHM1
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / voltage-gated calcium channel activity / monoatomic cation channel activity / plasma membrane / Calcium homeostasis modulator 1
Function and homology information
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRen Y / Yang X / Shen YQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91954119 China
CitationJournal: J Biol Chem / Year: 2022
Title: Cryo-EM structure of the heptameric calcium homeostasis modulator 1 channel.
Authors: Yue Ren / Yang Li / Yaojie Wang / Tianlei Wen / Xuhang Lu / Shenghai Chang / Xing Zhang / Yuequan Shen / Xue Yang /
Abstract: Calcium homeostasis modulator 1 (CALHM1) is a voltage- and Ca-gated ATP channel that plays an important role in neuronal signaling. However, as the previously reported CALHM structures are all in the ...Calcium homeostasis modulator 1 (CALHM1) is a voltage- and Ca-gated ATP channel that plays an important role in neuronal signaling. However, as the previously reported CALHM structures are all in the ATP-conducting state, the gating mechanism of ATP permeation is still elusive. Here, we report cryo-EM reconstructions of two Danio rerio CALHM1 heptamers with ordered or flexible long C-terminal helices at resolutions of 3.2 Å and 2.9 Å, respectively, and one D. rerio CALHM1 octamer with flexible long C-terminal helices at a resolution of 3.5 Å. Structural analysis shows that the heptameric CALHM1s are in an ATP-nonconducting state with a central pore diameter of approximately 6.6 Å. Compared with those inside the octameric CALHM1, the N-helix inside the heptameric CALHM1 is in the "down" position to avoid steric clashing with the adjacent TM1 helix. Molecular dynamics simulations show that as the N-helix moves from the "down" position to the "up" position, the pore size of ATP molecule permeation increases significantly. Our results provide important information for elucidating the mechanism of ATP molecule permeation in the CALHM1 channel.
History
DepositionDec 30, 2020-
Header (metadata) releaseJan 5, 2022-
Map releaseJan 5, 2022-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.209
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.209
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dse
  • Surface level: 0.209
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dse
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30832.png

Downloads & links

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Map

FileDownload / File: emd_30832.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 260 pix.
= 263.64 Å		1.01 Å/pix.
x 260 pix.
= 263.64 Å		1.01 Å/pix.
x 260 pix.
= 263.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.209 / Movie #1: 0.209
Minimum - Maximum-0.65123194 - 1.5689428
Average (Standard dev.)-0.002079409 (±0.056512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 263.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z263.640263.640263.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.6511.569-0.002

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Supplemental data

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Sample components

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Entire : CALHM1

EntireName: CALHM1
Components
  • Organelle or cellular component: CALHM1
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CALHM1

SupramoleculeName: CALHM1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)

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Macromolecule #1: Calcium homeostasis modulator 1

MacromoleculeName: Calcium homeostasis modulator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 41.213645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LEQKLISEED LRSDKFRIMV QFLQANQESF MNGICGIMAL ASAQMYSSFE FTCPCLPDYN YAYGIGILIV PPIWFFLLGY VMNNNISVL TEEWKRPVGK RSKDPAVLRY MFSSMTQRAL IAPAVWIAVT LMDGKSFLCA FSPTADLSEF VNESYQSLSQ K ELLKIQAK ...String:
LEQKLISEED LRSDKFRIMV QFLQANQESF MNGICGIMAL ASAQMYSSFE FTCPCLPDYN YAYGIGILIV PPIWFFLLGY VMNNNISVL TEEWKRPVGK RSKDPAVLRY MFSSMTQRAL IAPAVWIAVT LMDGKSFLCA FSPTADLSEF VNESYQSLSQ K ELLKIQAK IPCKDIFEEH EIISREAATR YIRCLSQACG WTFLMVITLV AFLVRAIRPC FTQAAFLKTK YWSHYIDTER KL FDETCKE HAKSFAKVCI QQYFESISGE IVSQLPQSPA KKGKGNKDED GEKQKSDEER LLGIRKEGDM NKVLWNWHTC KPP LLLSKR TEEMNGHAHL DTHSLTDERH TKKKAVVYYS KV

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab into from cryosparc v2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12671
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: NOT APPLICABLE

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